Package: mulea
Type: Package
Title: Enrichment Analysis Using Multiple Ontologies and False
        Discovery Rate
Version: 1.1.1
Authors@R: c(
    person("Cezary", "Turek", role =  "aut",
        comment = c(ORCID = "0000-0002-1445-5378")),
    person("Marton", "Olbei", role = "aut",
        comment = c(ORCID = "0000-0002-4903-6237")),
    person("Tamas", "Stirling", email = "stirling.tamas@gmail.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-8964-6443")),
    person("Gergely", "Fekete", role = "aut",
        comment = c(ORCID = "0000-0001-9939-4860")),
    person("Ervin", "Tasnadi", role = "aut",
        comment = c(ORCID = "0000-0002-4713-5397")),
    person("Leila", "Gul", role = "aut"),
    person("Balazs", "Bohar", role = "aut",
        comment = c(ORCID = "0000-0002-3033-5448")),
    person("Balazs", "Papp", role = "aut",
        comment = c(ORCID = "0000-0003-3093-8852")),
    person("Wiktor", "Jurkowski", role = "aut",
        comment = c(ORCID = "0000-0002-7820-1991")),
    person("Eszter", "Ari", role = c("aut", "cph"),
        comment = c(ORCID = "0000-0001-7774-1067")))
Description: Background - Traditional gene set enrichment analyses are
        typically limited to a few ontologies and do not account for
        the interdependence of gene sets or terms, resulting in
        overcorrected p-values. To address these challenges, we
        introduce mulea, an R package offering comprehensive
        overrepresentation and functional enrichment analysis. Results
        - mulea employs a progressive empirical false discovery rate
        (eFDR) method, specifically designed for interconnected
        biological data, to accurately identify significant terms
        within diverse ontologies. mulea expands beyond traditional
        tools by incorporating a wide range of ontologies, encompassing
        Gene Ontology, pathways, regulatory elements, genomic
        locations, and protein domains. This flexibility enables
        researchers to tailor enrichment analysis to their specific
        questions, such as identifying enriched transcriptional
        regulators in gene expression data or overrepresented protein
        domains in protein sets. To facilitate seamless analysis, mulea
        provides gene sets (in standardised GMT format) for 27 model
        organisms, covering 22 ontology types from 16 databases and
        various identifiers resulting in almost 900 files.
        Additionally, the muleaData ExperimentData Bioconductor package
        simplifies access to these pre-defined ontologies. Finally,
        mulea's architecture allows for easy integration of
        user-defined ontologies, or GMT files from external sources
        (e.g., MSigDB or Enrichr), expanding its applicability across
        diverse research areas. Conclusions - mulea is distributed as a
        CRAN R package. It offers researchers a powerful and flexible
        toolkit for functional enrichment analysis, addressing
        limitations of traditional tools with its progressive eFDR and
        by supporting a variety of ontologies. Overall, mulea fosters
        the exploration of diverse biological questions across various
        model organisms.
biocViews: Annotation, DifferentialExpression, GeneExpression,
        GeneSetEnrichment, GO, GraphAndNetwork, MultipleComparison,
        Pathways, Reactome, Software, Transcription, Visualization
License: GPL-2
Depends: R (>= 4.0.0)
Imports: data.table (>= 1.13.0), dplyr, fgsea (>= 1.0.2), ggplot2,
        ggraph (>= 2.0.3), magrittr (>= 2.0.3), methods, parallel (>=
        4.0.2), plyr (>= 1.8.4), Rcpp, readr, rlang, scales, stats,
        stringi, tibble, tidygraph, tidyverse
Suggests: devtools, knitr, rmarkdown, testthat (>= 3.1.4)
LinkingTo: Rcpp
VignetteBuilder: knitr
URL: https://github.com/ELTEbioinformatics/mulea
BugReports: https://github.com/ELTEbioinformatics/mulea/issues
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Encoding: UTF-8
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://eltebioinformatics.r-universe.dev
Date/Publication: 2026-01-26 11:29:53 UTC
RemoteUrl: https://github.com/eltebioinformatics/mulea
RemoteRef: HEAD
RemoteSha: e23181f37e54a51e57e746b372d6a187be0e79e7
NeedsCompilation: yes
Packaged: 2026-10-12 11:17:25 UTC; root
Author: Cezary Turek [aut] (ORCID: <https://orcid.org/0000-0002-1445-5378>),
  Marton Olbei [aut] (ORCID: <https://orcid.org/0000-0002-4903-6237>),
  Tamas Stirling [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8964-6443>),
  Gergely Fekete [aut] (ORCID: <https://orcid.org/0000-0001-9939-4860>),
  Ervin Tasnadi [aut] (ORCID: <https://orcid.org/0000-0002-4713-5397>),
  Leila Gul [aut],
  Balazs Bohar [aut] (ORCID: <https://orcid.org/0000-0002-3033-5448>),
  Balazs Papp [aut] (ORCID: <https://orcid.org/0000-0003-3093-8852>),
  Wiktor Jurkowski [aut] (ORCID: <https://orcid.org/0000-0002-7820-1991>),
  Eszter Ari [aut, cph] (ORCID: <https://orcid.org/0000-0001-7774-1067>)
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>